Dark matters: Contrasting responses of stream biofilm to browning and loss of riparian shading.

Concentrations of terrestrial-derived dissolved organic carbon (DOC) in freshwater ecosystems have increased consistently, causing freshwater browning. The mechanisms behind browning are complex, but in forestry-intensive regions browning is accelerated by land drainage. Forestry actions in streamside riparian forests alter canopy shading, which together with browning is expected to exert a complex and largely unpredictable control over key ecosystem functions. We conducted a stream mesocosm experiment with three levels of browning (ambient vs. moderate vs. high, with 2.7 and 5.5-fold increase, respectively, in absorbance) crossed with two levels of riparian shading (70% light reduction vs. open canopy) to explore the individual and combined effects of browning and loss of shading on the quantity (algal biomass) and nutritional quality (polyunsaturated fatty acid and sterol content) of the periphytic biofilm. We also conducted a field survey of differently colored (4.7 to 26.2 mg DOC L-1 ) streams to provide a 'reality check' for our experimental findings. Browning reduced greatly the algal biomass, suppressed the availability of essential polyunsaturated fatty acids, especially eicosapentaenoic acid (EPA), and sterols, but increased the availability of terrestrial-derived long-chain saturated fatty acids (LSAFA). In contrast, loss of shading increased primary productivity, which resulted in elevated sterol and EPA contents of the biofilm. The field survey largely repeated the same pattern: biofilm nutritional quality decreased significantly with increasing DOC, as indicated particularly by a decrease of the ω-3:ω-6 ratio and increase in LSAFA content. Algal biomass, in contrast, was mainly controlled by dissolved inorganic nitrogen (DIN) concentration, while DOC concentration was of minor importance. The ongoing browning process is inducing a dramatic reduction in the nutritional quality of the stream biofilm. Such degradation of the major high-quality food source available for stream consumers may reduce the trophic transfer efficiency in stream ecosystems, potentially extending across the stream-forest ecotone.

Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch.

Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 single nucleotide polymorphisms, of which >10,000 were identified as potential candidates under selection (associated with >3000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate the multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.

Stochastic processes and ecological connectivity drive stream invertebrate community responses to short-term drought.

Community responses to and recovery from disturbances depend on local (e.g. presence of refuges) and regional (connectivity to recolonization sources) factors. Droughts are becoming more frequent in boreal regions, and are likely to constitute a severe disturbance for boreal stream communities where organisms largely lack adaptations to such hydrological extremes. We conducted an experiment in 24 semi-natural stream flumes to assess the effects of local and regional factors on the responses of benthic invertebrate communities to a short-term drought. We manipulated flow (drought vs. constant-flow), spatial arrangement of leaf litter patches (aggregated vs. evenly distributed) and colonization from regional species pool (enhanced vs. ambient connectivity) to test the combined effects of disturbance, resource arrangement and connectivity on the structural and functional responses of benthic invertebrate communities. We found that a drought as short as 1 week reduced invertebrate taxonomic richness and abundance, mainly through stochastic extinctions. Such changes in richness were not reflected in functional diversity. This suggests that communities were characterized by a high degree of functional redundancy, which allowed maintenance of functional diversity despite species losses. Feeding groups responded differently to drought, with organic matter decomposers responding more than scrapers and predators. Three weeks were insufficient for complete invertebrate community recovery from drought. However, recovery was greater in channels subjected to enhanced connectivity, which increased taxonomic diversity and abundance of certain taxa. Spatial configuration of resources explained the least variation in our response variables, having a significant effect only on invertebrate abundance and evenness (both sampling occasions) and taxonomic richness (end of recovery period). Even a short drought, if occurring late in the season, may not allow communities to recover before the onset of winter, thus having a potentially long-lasting effect on stream communities. For boreal headwaters, extreme dewatering poses a novel disturbance regime that may trigger substantial and potentially irreversible changes. An improved understanding of such changes is needed to underpin adaptive management strategies in these increasingly fragmented and disturbed ecosystems.

Quantifying and addressing the prevalence and bias of study designs in the environmental and social sciences.

Building trust in science and evidence-based decision-making depends heavily on the credibility of studies and their findings. Researchers employ many different study designs that vary in their risk of bias to evaluate the true effect of interventions or impacts. Here, we empirically quantify, on a large scale, the prevalence of different study designs and the magnitude of bias in their estimates. Randomised designs and controlled observational designs with pre-intervention sampling were used by just 23% of intervention studies in biodiversity conservation, and 36% of intervention studies in social science. We demonstrate, through pairwise within-study comparisons across 49 environmental datasets, that these types of designs usually give less biased estimates than simpler observational designs. We propose a model-based approach to combine study estimates that may suffer from different levels of study design bias, discuss the implications for evidence synthesis, and how to facilitate the use of more credible study designs.

Habitat patchiness, ecological connectivity and the uneven recovery of boreal stream ecosystems from an experimental drought.

Ongoing climate change is increasing the occurrence and intensity of drought episodes worldwide, including in boreal regions not previously regarded as drought prone, and where the impacts of drought remain poorly understood. Ecological connectivity is one factor that might influence community structure and ecosystem functioning post-drought, by facilitating the recovery of sensitive species via dispersal at both local (e.g. a nearby habitat patch) and regional (from other systems within the same region) scales. In an outdoor mesocosm experiment, we investigated how impacts of drought on boreal stream ecosystems are altered by the spatial arrangement of local habitat patches within stream channels, and variation in ecological connectivity with a regional species pool. We measured basal ecosystem processes underlying carbon and nutrient cycling: (a) algal biomass accrual; (b) microbial respiration; and (c) decomposition of organic matter, and sampled communities of aquatic fungi and benthic invertebrates. An 8-day drought event had strong impacts on both community structure and ecosystem functioning, including algal accrual, leaf decomposition and microbial respiration, with many of these impacts persisting even after water levels had been restored for 3.5 weeks. Enhanced connectivity with the regional species pool and increased aggregation of habitat patches also affected multiple response variables, especially those associated with microbes, and in some cases reduced the effects of drought to a small extent. This indicates that spatial processes might play a role in the resilience of communities and ecosystem functioning, given enough time. These effects were however insufficient to facilitate significant recovery in algal growth before seasonal dieback began in autumn. The limited resilience of ecosystem functioning in our experiment suggests that even short-term droughts can have extended consequences for stream ecosystems in the world's vast boreal region, and especially on the ecosystem processes and services mediated by algal biofilms.

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation.

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

Comparison of Migratory and Resident Populations of Brown Trout Reveals Candidate Genes for Migration Tendency.

Candidate genes associated with migration have been identified in multiple taxa: including salmonids, many of whom perform migrations requiring a series of physiological changes associated with the freshwater-saltwater transition. We screened over 5,500 SNPs for signatures of selection related to migratory behavior of brown trout Salmo trutta by focusing on ten differentially migrating freshwater populations from two watersheds (the Koutajoki and the Oulujoki). We found eight outlier SNPs potentially associated with migratory versus resident life history using multiple (≥3) outlier detection approaches. Comparison of three migratory versus resident population pairs in the Koutajoki watershed revealed seven outlier SNPs, of which three mapped close to genes ZNF665-like, GRM4-like, and PCDH8-like that have been previously associated with migration and smoltification in salmonids. Two outlier SNPs mapped to genes involved in mucus secretion (ST3GAL1-like) and osmoregulation (C14orf37-like). The last two strongly supported outlier SNPs mapped to thermally induced genes (FNTA1-like, FAM134C-like). Within the Oulujoki, the only consistent outlier SNP mapped close to a gene (EZH2) that is associated with compensatory growth in fasted trout. Our results suggest that a relatively small yet common set of genes responsible for physiological functions associated with resident and migratory life histories is evolutionarily conserved.

Combined effects of local habitat, anthropogenic stress, and dispersal on stream ecosystems: a mesocosm experiment.

The effects of anthropogenic stressors on community structure and ecosystem functioning can be strongly influenced by local habitat structure and dispersal from source communities. Catchment land uses increase the input of fine sediments into stream channels, clogging the interstitial spaces of benthic habitats. Aquatic macrophytes enhance habitat heterogeneity and mediate important ecosystem functions, being thus a key component of habitat structure in many streams. Therefore, the recovery of macrophytes following in-stream habitat modification may be prerequisite for successful stream restoration. Restoration success is also affected by dispersal of organisms from the source community, with potentially the strongest responses in relatively isolated headwater sites that receive a limited amount of dispersing individuals. We used a factorial design in a set of stream mesocosms to study the independent and combined effects of an anthropogenic stressor (sand sedimentation), local habitat (macrophytes, i.e., moss transplants), and enhanced dispersal (two levels: high vs. low) on organic matter retention, algal accrual rate, leaf decomposition, and macroinvertebrate community structure. Overall, all responses were simple additive effects with no interactions between treatments. Sand reduced algal accumulation, total invertebrate density, and density of a few individual taxa. Mosses reduced algal accrual rate and algae-grazing invertebrates, but enhanced organic matter retention and the number of detritus and filter feeders. Mosses also reduced macroinvertebrate diversity by increasing the dominance by a few taxa. Mosses reduced leaf mass loss, possibly because the organic matter retained by mosses provided an additional food source for leaf-shredding invertebrates and thus reduced shredder aggregation into leaf packs. The effect of mosses on macroinvertebrate communities and ecosystem functioning was distinct irrespective of the level of dispersal, suggesting strong environmental control of community structure. The strong environmental control of macroinvertebrate community composition even under enhanced dispersal suggests that re-establishing key habitat features, such as natural stream vegetation, could aid ecosystem recovery in boreal streams.

First record of proliferative kidney disease agent Tetracapsuloides bryosalmonae in wild brown trout and European grayling in Finland.

The myxozoan endoparasite Tetracapsuloides bryosalmonae causes temperature-driven proliferative kidney disease (PKD) in salmonid fishes. Despite the economic and ecological importance of PKD, information about the distribution of the parasite is still scarce. Here, we report for the first time the occurrence of T. bryosalmonae in wild brown trout Salmo trutta and European grayling Thymallus thymallus populations in Finland. We detected T. bryosalmonae at high prevalence in both brown trout and European grayling from the transboundary Finnish-Russian River Koutajoki system (Rivers Oulankajoki, Kuusinkijoki, Kitkajoki, Maaninkajoki, and Juumajoki) in north-eastern Finland. In southern Finland, T. bryosalmonae was detected in River Siuntionjoki young-of-the-year brown trout collected both in 2015 and 2016 (100% prevalence), while the parasite was not observed in fish from 3 other rivers (Ingarskila, Mustajoki, and Vantaanjoki) flowing to the Gulf of Finland. Our results, together with those from recent studies of Atlantic salmon, indicate that T. bryosalmonae is distributed over much higher latitudes in northern Europe than previously appreciated. We expect that increasing water temperatures will likely cause new PKD outbreaks in these more northerly regions in the future.

Sediments and flow have mainly independent effects on multitrophic stream communities and ecosystem functions.

Stream ecosystems are affected by multiple abiotic stressors, and species responses to simultaneous stressors may differ from those predicted based on single-stressor responses. Using 12 semi-natural stream channels, we examined the individual and interactive effects of flow level (low or high flow) and addition of fine sediments (grain size <2 mm) on key ecosystem processes (leaf breakdown, algal biomass accrual) and benthic macroinvertebrate and fungal communities. Both stressors had mostly independent effects on biological responses, with sand addition being the more influential of the two. Sand addition decreased algal biomass and microbe-mediated leaf breakdown significantly, whereas invertebrate shredder-mediated breakdown only responded to flow level. Macroinvertebrate community composition responded significantly to both stressors. Fungal biomass decreased and shredder abundance increased when sand was added; thus, organisms at different trophic levels can exhibit highly variable responses to the same stressor. Terrestrial endophytic fungi were abundant in low-flow flumes where leaf mass loss was also highest, indicating that terrestrial endophytes may contribute importantly to leaf decomposition in the aquatic environment. Leaf breakdown rates depended on the identity and abundance of the dominant decomposer species, suggesting that the effects of anthropogenic activities on ecosystem processes may be driven by changes in the abundance of a few key species. The few observed interactive effects were all antagonistic (i.e., less than the sum of the individual effects); for example, increased flow stimulated algal biomass accumulation but this effect was largely cancelled by sand. While our finding that sand and stream flow did not have strong synergistic effects can be considered reassuring for management, future experiments should manipulate these and other human stressors in experiments that run for much longer periods, thus focusing on the long-term impacts of multiple simultaneously operating stressors.

Twenty years of stream restoration in Finland: little response by benthic macroinvertebrate communities.

The primary focus of many in-stream restoration projects is to enhance habitat diversity for salmonid fishes, yet the lack of properly designed monitoring studies, particularly ones with pre-restoration data, limits any attempts to assess whether restoration has succeeded in improving salmonid habitat. Even less is known about the impacts of fisheries-related restoration on other, non-target biota. We examined how restoration aiming at the enhancement of juvenile brown trout (Salmo trutta L.) affects benthic macroinvertebrates, using two separate data sets: (1) a before-after-control-impact (BACI) design with three years before and three after restoration in differently restored and control reaches of six streams; and (2) a space-time substitution design including channelized, restored, and near-natural streams with an almost 20-year perspective on the recovery of invertebrate communities. In the BACI design, total macroinvertebrate density differed significantly from before to after restoration. Following restoration, densities decreased in all treatments, but less so in the controls than in restored sections. Taxonomic richness also decreased from before to after restoration, but this happened similarly in all treatments. In the long-term comparative study, macroinvertebrate species richness showed no difference between the channel types. Community composition differed significantly between the restored and natural streams, but not between restored and channelized streams. Overall, the in-stream restoration measures used increased stream habitat diversity but did not enhance benthic biodiversity. While many macroinvertebrates may be dispersal limited, our study sites should not have been too distant to reach within almost two decades. A key explanation for the weak responses by macroinvertebrate communities may have been historical. When Fennoscandian streams were channelized for log floating, the loss of habitat heterogeneity was only partial. Therefore, habitat may not have been limiting the macroinvertebrate communities to begin with. Stream restoration to support trout fisheries has strong public acceptance in Finland and will likely continue to increase in the near future. Therefore, more effort should be placed on assessing restoration success from a biodiversity perspective using multiple organism groups in both stream and riparian ecosystems.

Does the introduced brook trout (Salvelinus fontinalis) affect growth of the native brown trout (Salmo trutta)?

Non-native brook trout have become widely established in North European streams. We combined evidence from an artificial-stream experiment and drainage-scale field surveys to examine whether brook trout suppressed the growth of the native brown trout (age 0 to age 2). Our experimental results demonstrated that brown trout were unaffected by the presence of brook trout but that brook trout showed reduced growth in the presence of brown trout. However, the growth reduction only appeared in the experimental setting, indicating that the reduced spatial constraint of the experimental system may have forced the fish to unnaturally intense interactions. Indeed, in the field, no effect of either species on the growth of the putative competitor was detected. These results caution against uncritical acceptance of findings from small-scale experiments because they rarely scale up to more complex field situations. This and earlier work suggest that the establishment of brook trout in North European streams has taken place mainly because of the availability of unoccupied (or underutilized) niche space, rather than as a result of species trait combinations or interspecific competition per se.

Niche characteristics explain the reciprocal invasion success of stream salmonids in different continents.

An ability to understand and predict invasions is elemental for controlling the detrimental effects of introduced organisms on native biota. In eastern North America, European brown trout generally dominates over, and eventually replaces, the native brook trout. We show here that in northern Europe the pattern of replacement between these two species is reversed: when transferred to North European streams, brook trout spread extensively and partially replaced the native brown trout. The effect of brook trout on brown trout was habitat-specific: brook trout excluded the native species only in small tributary streams where the reproduction of brown trout was severely reduced, whereas in larger streams brown trout was largely unaffected. Thus, the pattern of coexistence among the two salmonids in our study area is approaching that typically observed in North American streams. In both areas, brook trout ultimately settles in small headwater streams, but the process of replacement differs profoundly: in North Europe, brook trout replaces brown trout in headwater streams, whereas in North America these same streams are the ultimate refuge area for brook trout under the invasion pressure by brown trout. Our results underline the importance of knowing species' niche characteristics to explain and predict biological invasions.